BIOLOGICAL SYSTEMATICS AND EVOLUTIONARY THEORY

BIOLOGICAL SYSTEMATICS AND EVOLUTIONARY THEORYbyAleta QuinnBA, University of Maryland, 2005BS, University of Maryland, 2005Submitted to the Graduate Faculty ofThe Kenneth P. Dietrich School of Arts and Sciences in partial fulfillmentof the requirements for the degree ofDoctor of PhilosophyUniversity of Pittsburgh2015

UNIVERSITY OF PITTSBURGHKENNETH P. DIETRICH SCHOOL OF ARTS AND SCIENCESThis dissertation was presentedbyAleta QuinnIt was defended onJuly 1, 2015and approved byJames Lennox, PhD, History & Philosophy of ScienceSandra Mitchell, PhD, History & Philosophy of ScienceKenneth Schaffner, PhD, History & Philosophy of ScienceJeffrey Schwartz, PhD, AnthropologyDissertation Director: James Lennox, PhD, History & Philosophy of Scienceii

Copyright by Aleta Quinn2015iii

BIOLOGICAL SYSTEMATICS AND EVOLUTIONARY THEORYAleta Quinn, PhDUniversity of Pittsburgh, 2015In this dissertation I examine the role of evolutionary theory in systematics (the science that discoversbiodiversity). Following Darwin’s revolution, systematists have aimed to reconstruct the past. My dissertationanalyzes common but mistaken assumptions about sciences that reconstruct the past by tracing theassumptions to J.S. Mill. Drawing on Mill’s contemporary, William Whewell, I critique Mill’s assumptions anddevelop an alternative and more complete account of systematic inference as inference to the bestexplanation.First, I analyze the inadequate view: that scientists use causal theories to hypothesize what past chainsof events must have been, and then form hypotheses that identify segments of a network of events and causaltransactions between events. This model assumes that scientists can identify events in the world by referenceto neatly delineated properties, and that discovering causal laws is simply a matter of testing what regularitieshold between events so delineated. Twentieth century philosophers of science tacitly adopted this assumptionin otherwise distinct models of explanation. As Whewell pointed out in his critique of Mill, the problem withthis assumption is that the delineation of events via properties is itself the hard part of science.Drawing on Whewell’s philosophy of science, and my work as a member of a team of systematistsrevising the genus Bassaricyon, I show how historical scientists avoid the problems of the inadequate view.Whewell’s account of historical science and of consilience provide a better foothold for understandingsystematics. Whewell’s consilience describes the fit between a single hypothesis and lines of reasoning thatdraw on distinct conceptual structures.My analysis clarifies the significance of two revolutions in systematics. Whereas pre-Darwiniansystematists used consilience as an evidentiary criterion without explicit justification, after Darwin’s revolutioniv

consilience can be understood as a form of inference to the best explanation. I show that the adoption ofHennig’s phylogenetic framework formalized methodological principles at the core of Whewell’sphilosophy of historical science. I conclude by showing how two challenges that are frequently pressedagainst inference to the best explanation are met in the context of phylogenetic inference.v

TABLE OF CONTENTSPREFACE . ix1.0 INTRODUCTION . 12.0 MILL’S PHILOSOPHY OF SCIENCE. 62.1 MILL’S INDUCTION AND CAUSAL REASONING . 62.1.1 Induction: Particulars and General Propositions . 62.1.2 Justifying Induction: Causal Necessity. 122.1.3 Justifying Induction: Relevant Resemblances. 212.1.4 Mill’s Causal Ontology . 232.2 NATURAL KINDS . 242.2.1 Mill on Natural Kinds . 242.2.2 Scientific Investigation: Biological Natural Kinds . 312.2.3 Justifying Mill’s Natural Kinds . 353.0 WHEWELL’S PHILOSOPHY OF SCIENCE . 403.1 WHEWELL’S INDUCTION AND CRITIQUE OF MILL . 413.1.1 The Role of Concepts in Science . 413.1.2 Concepts and Causes in Kepler’s Discovery . 463.1.3 Concepts and Causes in Classificatory Science . 513.2 WHEWELL ON NATURAL AFFINITY . 533.2.1 Goals and Problems of Classification . 533.2.2 Successful Classificatory Science . 613.2.3 Justifying Natural Affinity . 65vi

3.3 WHEWELL’S NATURAL THEOLOGY . 684.0 NETWORK ASSUMPTIONS AND THE RELEVANCE PROBLEM . 734.1 THE NETWORK ASSUMPTIONS AND MODELS OF EXPLANATION . 744.1.1 The Network Assumptions and the Covering Law Model . 744.1.2 The Network Assumptions and Historical Explanation . 764.2 THE NETWORK ASSUMPTIONS AND THE RELEVANCE PROBLEM . 824.2.1 The ‘Hard Part’ Objection . 824.2.2 The Conceptual Structure of Science . 864.2.3 Event Chains and Historical Hypotheses . 905.0 HISTORICAL HYPOTHESES . 955.1 HISTORICAL HYPOTHESES AND CAUSAL DEPENDENCE . 965.1.1 Historical Causal Reasoning . 965.1.2 Historical Hypotheses and Whewell’s Practice of Historical Architecture. 1015.2 SYSTEMATICS AS HISTORICAL SCIENCE . 1085.2.1 Lamarck and Gegenbaur. 1085.2.2 Hennig’s Methodology and Tree Diagrams . 1126.0 PHYLOGENETIC INFERENCE TO THE BEST EXPLANATION . 1236.1 THE UNDERCONSIDERATION OBJECTION AND THE PROBLEM OF EVIDENCE . 1256.2 CONSILIENCE AND THE TAUTOLOGY OBJECTION . 1417.0 CONCLUSION . 158BIBLIOGRAPHY . 160vii

LIST OF FIGURES5.1. A square space with equal semicircular arches. Whewell's (1830) plate I, figure 1. . 1035.2. Church with two side aisles and only semicircular vaults. Whewell’s (1830) plate IV, figure 6. . 1045.3. Vaulting a rectangular space using pointed and semicircular arches. Whewell's plate I, figure 3. 1055.4. Gray shading indicates proposed groupings. At left, a monophyletic group (clade). Center, a paraphyleticgroup. At right, a polyphyletic group. . 1135.5. At left, the paraphyletic group [B, C]. At center, [B, C] is now polyphyletic . 1145.6. At left, the polyphyletic group [B, D]. At right, the group [B, D] is rendered paraphyletic . 1145.7. Possession of m is synapomorphic similarity. At center, trait p is autapomorphic in taxon A. At right, traitq arose as an autapomorphy in taxon B and trait r as an autapomorphy in taxon D . 1155.8. Relationships within Bassaricyon, the olingos and Olinguito. 1195.9. An invalid tree diagram. 1205.10. Apomorphic characters within Bassaricyon . 1216.1. The set of possible 3-taxon bifurcating trees for three organisms designated A, B, and C . 1296.2. Morphometric analysis of 55 specimens referred to Bassaricyon. 1486.3. Morphometric analysis of specimens referred to Bassaricyon excluding B. neblina . 1496.4. Maximum likelihood analysis of relationships in the clade that includes Bassaricyon and Nasua . 1506.5. Relationships of Bassaricyon species. . 151viii

PREFACEI am deeply grateful to Jim Lennox for all of his guidance, feedback, and encouragement. I thankhim for getting me through this dissertation and also for his assistance in many other aspects of thephilosophical life.I thank my committee, Sandy Mitchell, Ken Schaffner, and Jeff Schwartz, for their supportwith this dissertation and throughout my graduate career. For guidance on (and enthusiasm about)technical systematics matters in particular I owe a debt of gratitude to Jeff. In the same vein I thankKevin de Queiroz for comments on chapter six, and also for many interactions that benefitted theremainder of the dissertation as well as other projects.It is difficult to imagine how things would have gone without STARS who providedcomments, discussions, and moral support: Julia Bursten, Peter Distelzweig, Bihui Li, ElizabethO’Neill, Catherine Stinson, Kathryn Tabb, and Karen Zweir. I thank also other colleagues in theextraordinary University of Pittsburgh HPS community including Meghan Dupree, Yoichi Ishida,Aaron Novick, and Elay Shech. I thank Rita Levine, Joann McIntyre, and Natalie Schweninger foradministrative support, and Edouard Machery for assistance and advice.Others in the professional history and philosophy community have also been extremelyhelpful. Pamela Henson has been an invaluable source for advice as well as information on thehistory of systematics. Others in the DC History and Philosophy of Biology reading group, includingLindley Darden and Eric Saidel, provided comments and critical discussion of chapter 4. I thankaudiences with whom I discussed portions of the dissertation at the 2014 Joint PSA/HSS Meetings,the 21st Annual Kent State May 4th Philosophy Graduate Student Conference, the 2014 NorthCarolina Philosophical Society Meeting, and the 2013 Western Michigan University GraduatePhilosophy Conference.ix

Chapter six in particular required the assistance of Smithsonian systematists. I thank theother members of Team Olinguito, especially Kris Helgen and Don Wilson (who first introducedme to the systematics community, all those years ago). I have benefitted greatly from other staff andvisiting researchers at the Smithsonian Institution, among them Carole Baldwin, Bruce Collette,Harry Greene, Dave Johnson, Celeste Luna, Roy McDiarmid, Jim Mead, Dan Mulcahy, Jim Murphy,Ai Nonaka, Neal Woodman, Kelly Zamudio, and George Zug. I thank them all for discussions andmoral support during the awesome task of completing and editing the text. My thanks also go toSmithsonian Librarians, especially Richard Greene, Gil Taylor, and Daria Wingreen-Mason, and staffand volunteers at the Smithsonian Archives. Richard, thanks also for POETS.Parts of the dissertation were completed with support from the University of PittsburghProvost’s Development Fund, and a Smithsonian Institution Predoctoral Fellowship. I am gratefulfor this support and for travel assistance from the Wesley C. Salmon Fund and the History ofScience Society.For help and encouragement at earlier stages in my career, I thank Matthias Frisch and JamesLesher, and most especially Chip Manekin, who is (apart from myself) most responsible for mychoice of career. Thanks also to Bob Donaldson who first introduced me to philosophy.I thank my brother, as well as Frank Balsinger, Gilberto Campello, Marianna Lima, andEmily McGinley. And Steve Carmody. It turns out you were right, I actually could do it.This dissertation is dedicated to my mother: well, we did it.x

1.0 INTRODUCTIONIn this dissertation I examine the role of evolutionary theory in systematics (the science thatdiscovers and studies biodiversity) by analyzing systematics qua historical science. FollowingDarwin’s revolution, systematists have aimed to reconstruct the past. I analyze historical science,focusing on historical causal reasoning, in order to show the relationship between evidence andhypotheses about what the past must have been like. I explicate the debate between John Stuart Milland William Whewell as it applies to these philosophical questions. Key assumptions of thesephilosophers framed subsequent understanding of historical science. Armed with this philosophicalframework, I analyze the conceptual foundations of modern systematics, as developed by WilliHennig, and explicate inference in systematics through consideration of a recent phylogenetic study.The dissertation concerns the following questions: what is the status of historical science?How do historical hypotheses express causal information, and how does historical inference rely oncausal reasoning? How do systematic methods reflect the historical nature of the science; how didsystematics become a historical science? How do systematists take account of evidence? How dobiological theories inform phylogenetic inference? How does the inter-theoretic nature ofsystematics play out in phylogenetic inference and in systematic hypotheses?There is a tendency to dismiss pre-Darwinian systematics as unscientific. It might bewondered what could possibly be gained through consideration of pre-Darwinian philosophy ofsystematics. In fact, pre-Darwinian systematics as ahistorical science provides an invaluable resourcefor understanding what it means that systematics is essentially historical. Systematics is an idealsubject for understanding historical scientific methodology precisely because we can study theintroduction of historicity to the science.1